3L3C	Rna Binding Protein Rna	date	Dec 16, 2009
title	Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bo Glc6p
authors	S.A.Strobel, J.C.Cochrane, S.V.Lipchock, K.D.Smith
compound		source
Molecule: U1 Small Nuclear Ribonucleoprotein A Chain: A, B, C, D Fragment: Rna Binding Domain Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11
Molecule: Rna (5'-R(Ap(A2m)Gpcpgpcpcpapgpapapcp Chain: E, F, G, H Engineered: Yes Mutation: Yes		Synthetic: Yes Other_details: Synthesized At Dharmacon
Molecule: Glms Ribozyme Chain: P, Q, R, S Engineered: Yes		Synthetic: Yes Other_details: In Vitro Transcribed From A Dna Template
symmetry	Space Group: P 1 21 1	R_factor 0.263 R_Free 0.303
crystal cell	length a length b length c angle alpha angle beta angle gamma 47.882 234.947 104.540 90.00 90.55 90.00
method	X-Ray Diffraction	resolution	2.85 Å
ligand	A2M, G6P, GTP, MG	enzyme
note	3L3C supersedes 3G95
Gene Ontology	Chain Function Process Component A, D, C, B nucleotide binding nucleic acid binding RNA binding protein binding snRNA binding mRNA splicing, via spliceoso... mRNA processing RNA splicing gene expression nucleus nucleoplasm spliceosomal complex ribonucleoprotein complex
Primary reference	Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme., Cochrane JC, Lipchock SV, Smith KD, Strobel SA, Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (322 Kb) [Save to disk] Biological Unit Coordinates (3l3c.pdb1.gz) 80 Kb Biological Unit Coordinates (3l3c.pdb2.gz) 81 Kb Biological Unit Coordinates (3l3c.pdb3.gz) 81 Kb Biological Unit Coordinates (3l3c.pdb4.gz) 81 Kb LPC: Ligand-Protein Contacts for 3L3C CSU: Contacts of Structural Units for 3L3C Structure Factors (724 Kb) Retrieve 3L3C in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3L3C from S2C, [Save to disk] Re-refined 3l3c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3L3C in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3L3C

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3L3C, from MSDmotif at EBI Fold representative 3l3c from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3l3c_A] [3l3c_B] [3l3c_C] [3l3c_D] [3l3c_E] [3l3c_F] [3l3c_G] [3l3c_H] [3l3c_P] [3l3c_Q] [3l3c_R] [3l3c_S] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Alignments of the sequence of 3L3C with the sequences similar proteins can be viewed for 3L3C's classification [SNRPA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3L3C

Community annotation for 3L3C at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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